django_simple/todo/jobfiles.py

   1 import logging
   2
   3 from django.db.models.signals import post_save, post_delete
   4 from django.dispatch import receiver
   5 from .models import Task
   6 import os
   7 import shutil
   8 import subprocess
   9 import json
  10 from string import Template
  11 import textwrap
  12
  13 logging.basicConfig()
  14 logger = logging.getLogger(__name__)
  15
  16 def write_ssbond(ssbond):
  17    list=[]
  18    if ssbond!='':
  19      ssbond=json.loads(ssbond)
  20      for e in ssbond:
  21            list.append(e[0])
  22            list.append(e[1])
  23      list_sorted=sorted(list)
  24
  25    if len(list)>0:
  26        return str(len(list))+' '+' '.join(map(str,list_sorted))+'\n'+\
  27             str(len(ssbond))+' '+' '.join(map(str,list))+'\n'
  28    else:
  29        return '0\n'
  30
  31
  32 @receiver(post_save, sender=Task)
  33 def write_on_task_save(sender, instance, **kwargs):
  34    if instance.ready and not instance.done and instance.running==0:
  35      if (not os.path.isdir(instance.jobdirname)):
  36         os.mkdir(instance.jobdirname)
  37 #     os.chdir(instance.jobdirname)
  38
  39
  40
  41 #md=Template('nstep=$nstep ntwe=100  ntwx=100   dt=0.20 damax=10.0 lang=1'+
  42 #   't_bath=300 reset_vel=0 respa ntime_split=1 maxtime_split=512 mdpdb')
  43 #wrapper = textwrap.TextWrapper(width=70)
  44 #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
  45
  46      if  instance.unres_ff =='E0LL2Y':
  47       w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954              &
  48 WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000        &
  49 WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000    &
  50 WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25                                        &
  51 CUTOFF=7.00000 WCORR4=0.00000
  52 """
  53      else:
  54       w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542              &
  55 WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000        &
  56 WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000    &
  57 WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000                      &
  58 CUTOFF=7.00000 WCORR4=0.00000
  59 """
  60
  61
  62      with open(instance.jobdirname+'/file.inp','w') as f:
  63        f.write(instance.name + ' UNRES server job'+ '\n')
  64
  65        if instance.type == 'min' :
  66
  67           control_line = 'SEED='+str(instance.md_seed)+' ' \
  68              + instance.min_choice \
  69              + ' pdbstart pdbref BOXX=1000. BOXY=1000. BOXZ=1000. '
  70           if not instance.min_overlap:
  71             control_line = control_line+'overlap '
  72           if not instance.min_searchsc:
  73             control_line = control_line+'nosearchsc '
  74           if instance.min_pdbout:
  75             control_line = control_line+'pdbout '
  76           if instance.min_unres_pdb:
  77             control_line = control_line+'unres_pdb '
  78
  79           type_line = 'print_min_ini print_min_res print_min_stat'\
  80             +' MAXMIN='+str(instance.min_maxmin)\
  81             +' MAXFUN='+str(instance.min_maxfun)
  82
  83
  84        seq=instance.md_seq.replace(" ","")
  85        dimen3=len(seq)
  86        if dimen3>1:
  87           if seq[0]=='X':
  88             dimen3-=1
  89           if seq[-1]=='X':
  90             dimen3-=1
  91
  92        nogly ='CDSQKIPTFNHLRWAVEYM'
  93        seq2 = ''.join([c for c in seq if c in nogly])
  94
  95        dimen3=(dimen3+len(seq2))*3
  96
  97
  98        if instance.type == 'md' :
  99           control_line = 'SEED='+str(instance.md_seed)+' '\
 100            +instance.md_start +' md one_letter BOXX=1000. BOXY=1000. BOXZ=1000. '
 101           if instance.md_pdbref:
 102              control_line = control_line+'pdbref '
 103
 104           type_line = 'reset_vel=0'\
 105              +' t_bath='+str(instance.md_temp)\
 106              +' nstep='+str(instance.md_nstep)\
 107              +' ntwe='+str(instance.md_ntwe)\
 108              +' ntwx='+str(instance.md_ntwx)\
 109              +' dt='+str(instance.md_dt)
 110           if instance.md_lang == 'langevin':
 111             type_line = type_line + ' lang=1 '
 112             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 113           if instance.md_lang == 'berendsen':
 114             type_line = type_line + ' lang=0 tbf '
 115             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 116           if instance.md_respa:
 117             type_line = type_line + ' respa '
 118           if instance.md_mdpdb:
 119             type_line = type_line + ' mdpdb '
 120
 121        if instance.type == 'remd' :
 122           control_line = 'SEED='+str(instance.md_seed)+' '\
 123            +instance.md_start +' re one_letter BOXX=1000. BOXY=1000. BOXZ=1000. '
 124           if instance.md_pdbref:
 125              control_line = control_line+'pdbref '
 126
 127
 128           type_line = 'reset_vel='+ str(instance.remd_nstex)\
 129              +' nstep='+str(instance.md_nstep)\
 130              +' ntwe='+str(instance.md_ntwe)\
 131              +' ntwx='+str(instance.md_ntwx)\
 132              +' dt='+str(instance.md_dt)
 133           if instance.md_lang == 'langevin':
 134             type_line = type_line + ' lang=1 '
 135             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 136           if instance.md_lang == 'berendsen':
 137             type_line = type_line + ' lang=0 tbf '
 138             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 139           if instance.md_respa:
 140             type_line = type_line + ' respa '
 141           if instance.md_mdpdb:
 142             type_line = type_line + ' mdpdb '
 143
 144           type_line2 = 'nrep='+str(instance.remd_nrep) \
 145              +' nstex='+str(instance.remd_nstex) \
 146              +' tlist mlist sync nsyn='+str(instance.remd_nstex)\
 147              +' traj1file  rest1file TRAJCACHE=200'
 148
 149        if instance.md_start == 'pdbstart':
 150              type_line = type_line + ' preminim cart'
 151
 152        wrapper = textwrap.TextWrapper(width=70)
 153
 154        word_list = wrapper.wrap(text=control_line)
 155        for element in word_list[:-1]:
 156            f.write('{:79}'.format(element)+'&\n')
 157        f.write(word_list[-1]+'\n')
 158
 159        word_list = wrapper.wrap(text=type_line)
 160        for element in word_list[:-1]:
 161            f.write('{:79}'.format(element)+'&\n')
 162        f.write(word_list[-1]+'\n')
 163
 164        if instance.md_start == 'pdbstart':
 165          f.write('print_min_ini print_min_res print_min_stat\n')
 166
 167
 168        if instance.type == 'remd' :
 169           word_list = wrapper.wrap(text=type_line2)
 170           for element in word_list[:-1]:
 171               f.write('{:79}'.format(element)+'&\n')
 172           f.write(word_list[-1]+'\n')
 173
 174           tmp1=json.loads(instance.remd_multi_t)
 175           string1=" "
 176           word_list = wrapper.wrap(text=string1.join(tmp1))
 177           for element in word_list[:-1]:
 178               f.write('{:79}'.format(element)+'&\n')
 179           f.write(word_list[-1]+'\n')
 180
 181           tmp1=json.loads(instance.remd_multi_m)
 182           string1=" "
 183           word_list = wrapper.wrap(text=string1.join(tmp1))
 184           for element in word_list[:-1]:
 185               f.write('{:79}'.format(element)+'&\n')
 186           f.write(word_list[-1]+'\n')
 187
 188        f.write(w)
 189
 190
 191        if instance.type == 'min' or instance.md_start == 'pdbstart':
 192           f.write('plik.pdb\n')
 193           f.write(write_ssbond(instance.ssbond))
 194           f.write('0\n')
 195
 196
 197        if instance.type == 'md' and instance.md_start != 'pdbstart':
 198
 199           if instance.md_pdbref:
 200              f.write('plik.pdb\n')
 201           f.write(str(len(seq))+'\n')
 202           for i in range(0,len(seq),80):
 203              f.write(seq[i:i+80]+'\n')
 204           f.write('0\n0\n')
 205
 206        if instance.type == 'remd' and instance.md_start != 'pdbstart':
 207
 208           if instance.md_pdbref:
 209              f.write('plik.pdb\n')
 210           f.write(str(len(seq))+'\n')
 211           for i in range(0,len(seq),80):
 212              f.write(seq[i:i+80]+'\n')
 213           f.write('0\n0\n')
 214
 215
 216
 217
 218      if instance.type == 'min':
 219       os.chdir(instance.jobdirname)
 220       if  instance.unres_ff =='E0LL2Y':
 221         shutil.copy('../files/pbs.csh','.')
 222       else:
 223         shutil.copy('../files/pbs_new.csh','pbs.csh')
 224       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 225       os.chdir('..')
 226      elif instance.type == 'md':
 227       os.chdir(instance.jobdirname)
 228       if  instance.unres_ff =='E0LL2Y':
 229         f1 = open('../files/pbs_md.csh', 'r')
 230       else:
 231         f1 = open('../files/pbs_md_new.csh', 'r')
 232       f2 = open('pbs.csh', 'w')
 233       for line in f1:
 234            f2.write(line.replace('$dimen3',str(dimen3) ))
 235       f1.close()
 236       f2.close()
 237
 238       f1 = open('file.seq', 'w')
 239       for i in range(0,len(seq),80):
 240              f1.write(seq[i:i+80]+'\n')
 241       f1.close()
 242
 243       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 244       os.chdir('..')
 245      else:
 246 # instance.type == 'remd'
 247       tmp1=json.loads(instance.remd_multi_m)
 248       nreplicas=sum(map(int, tmp1))
 249 # hardcoded for 4 core nodes with FGPROC=2
 250       nodes=int(nreplicas*2/4)
 251       reszta = nreplicas*2-nodes*4
 252       if reszta == 0 :
 253         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4'
 254       else:
 255         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
 256
 257       tmp_ss=''
 258       ix=0
 259       if seq[0]=='X':
 260        ix=1
 261       if instance.ssbond!='':
 262         l=[]
 263         ss=json.loads(instance.ssbond)
 264         for e in ss:
 265            l.append(e[0]-ix)
 266            l.append(e[1]-ix)
 267         tmp_ss=' '.join(map(str,l))
 268
 269       os.chdir(instance.jobdirname)
 270       if  instance.unres_ff =='E0LL2Y':
 271         f1 = open('../files/pbs8.csh', 'r')
 272       else:
 273         f1 = open('../files/pbs8_new.csh', 'r')
 274       f2 = open('pbs8.csh', 'w')
 275       for line in f1:
 276           if '#PBS -l nodes=4:ppn=4' in line:
 277            f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
 278           elif '$ssbond' in line:
 279            f2.write(line.replace('$ssbond',tmp_ss))
 280           else:
 281            tmp1=json.loads(instance.remd_multi_t)
 282            f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
 283       f1.close()
 284       f2.close()
 285       os.chdir('..')
 286
 287 # write wham & cluster input
 288       with open(instance.jobdirname+'/file_wham.inp','w') as f:
 289           if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
 290               isampl=1
 291           else:
 292               isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
 293
 294           if instance.md_pdbref:
 295             f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
 296                ' einicheck=1 rescale=2 delta=0.02 cxfile classify\n')
 297           else:
 298             f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
 299               ' einicheck=1 rescale=2 delta=0.02 cxfile\n')
 300           f.write('nres='+str(len(seq))+' one_letter\n')
 301           for i in range(0,len(seq),80):
 302              f.write(seq[i:i+80]+'\n')
 303
 304           f.write(write_ssbond(instance.ssbond))
 305
 306
 307           f.write(w)
 308           f.write('\n')
 309           f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n')
 310           tmp1=json.loads(instance.remd_multi_t)
 311           for element in tmp1:
 312               f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
 313               f.write('kh= 0.0 Q0=0.0\n')
 314           rec=instance.md_nstep/instance.md_ntwx
 315           f.write('nfile_cx=1 rec_start='+str(rec/10)
 316                   +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
 317           f.write('file_MD000\n')
 318           if instance.md_pdbref:
 319              f.write('pdbref\n')
 320              f.write('plik.pdb\n')
 321
 322
 323       with open(instance.jobdirname+'/file_cluster.inp','w') as f:
 324           f.write(instance.name + ' UNRES server job'+ '\n')
 325           f.write('nres='+str(len(seq))
 326              +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
 327              +' temper='+str(instance.remd_cluter_temp)+'\n')
 328           f.write(w)
 329           for i in range(0,len(seq),80):
 330              f.write(seq[i:i+80]+'\n')
 331           f.write(write_ssbond(instance.ssbond))
 332
 333       os.chdir(instance.jobdirname)
 334       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 335       os.chdir('..')
 336
 337      print ret_code.stdout.readlines()
 338      logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
 339
 340 @receiver(post_delete, sender=Task)
 341 def delete_on_task_del(sender, instance, **kwargs):
 342    if instance.jobdirname:
 343       if os.path.isdir(instance.jobdirname):
 344          shutil.rmtree(instance.jobdirname)
 345          logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)
 346